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- PDB-7skq: BtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7skq | ||||||
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Title | BtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent inhibitor GRL-0617 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | HYDROLASE/INHIBITOR / Papain-like Protease / VIRAL PROTEIN / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() host cell membrane / viral genome replication / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / membrane => GO:0016020 / single-stranded RNA binding ...host cell membrane / viral genome replication / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / membrane => GO:0016020 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Freitas, B. / Durie, I. / Shepard, J. / O'Boyle, B. / Enos, S. / Pegan, S.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses. Authors: Freitas, B.T. / Ahiadorme, D.A. / Bagul, R.S. / Durie, I.A. / Ghosh, S. / Hill, J. / Kramer, N.E. / Murray, J. / O'Boyle, B.M. / Onobun, E. / Pirrone, M.G. / Shepard, J.D. / Enos, S. / ...Authors: Freitas, B.T. / Ahiadorme, D.A. / Bagul, R.S. / Durie, I.A. / Ghosh, S. / Hill, J. / Kramer, N.E. / Murray, J. / O'Boyle, B.M. / Onobun, E. / Pirrone, M.G. / Shepard, J.D. / Enos, S. / Subedi, Y.P. / Upadhyaya, K. / Tripp, R.A. / Cummings, B.S. / Crich, D. / Pegan, S.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.9 KB | Display | ![]() |
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PDB format | ![]() | 106 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1012 KB | Display | ![]() |
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Full document | ![]() | 1017.3 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7skrC ![]() 3e9sS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35875.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q0QDZ2, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium Acetate, 20% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 658061 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 0.756 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 3.15→3.2 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2484 / CC1/2: 0.602 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3E9S Resolution: 3.16→47.57 Å / SU ML: 0.5354 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.26 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.16→47.57 Å
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Refine LS restraints |
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LS refinement shell |
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